If Spies can prove he is as fast as Lorenzo then I would say it helps Rossi. Yamaha knows that it is only a matter of time before Rossi drops from the cutting edge, but his value as a marketing asset is far too great to ditch him in favor of Lorenzo. The lorenshow has already proved to be a problem child in his contract negotiations, manipulating the situation, dragging his feet, playing contract chicken. I can't see Japanese businessmen taking kindly to such behavior, even coming from what seems to be the Heir to the Throne. In the event they pick Lorenzo over Rossi, there is no guarantee Lorenzo will be content in the long term. He is chasing championships, and the second that bike (or the team situation in general) falls behind he will get the hell out. From this point of view Rossi is the clear choice for Yamaha, since Lorenzo is an unknown for the future whereas Rossi is happy developing a bike and retiring with the brand.
Rossi, however, is guilty of the same types of contract flip-flopping; he has a history of such actions when he left Honda, and his mouth is running again about Ducati. His mass appeal might make him still more valuable despite such animosity, and its easier to justify tolerating a whining 7 time premier class world champion than an upstart. Is Rossi winning races more valuable then Lorenzo winning championships? That is the question Yamaha needs to answer.
As for Spies, he appears to be far more loyal and obedient than Lorenzo. He really tried everything he could to stay in the suzuki family before making a switch. so his loyalty can be assured. If Spies reaches Lorenzo's level of on-track ability, Spies would be the superior choice. He carries relatively no baggage--just keep his mom happy. Spies' aforementioned loyalty and work ethic are a plus, and that looming 1000cc capacity change adds to his (and Rossi's for that matter) case. Assuming Spies=Lorenzo in the near future, then a Rossi/Spies garage seems better than a Spies/Lorenzo garage. Yamaha gets on track results from Spies and marketing appeal from Rossi without any intense #1 rider drama that Spies/Lorenzo would bring. The scenario laid out is crucially dependent on Spies finding a good deal more tenths however, so we shall see.